ePlant: visualizing and exploring multiple levels of data for hypothesis generation in plant biology

J Waese, J Fan, A Pasha, H Yu, G Fucile, R Shi… - The Plant …, 2017 - academic.oup.com
A big challenge in current systems biology research arises when different types of data must
be accessed from separate sources and visualized using separate tools. The high cognitive …

The impact of protein architecture on adaptive evolution

AF Moutinho, FF Trancoso… - Molecular biology and …, 2019 - academic.oup.com
Adaptive mutations play an important role in molecular evolution. However, the frequency
and nature of these mutations at the intramolecular level are poorly understood. To address …

Genomic insights into the evolution and ecology of botulinum neurotoxins

MJ Mansfield, AC Doxey - Pathogens and disease, 2018 - academic.oup.com
Clostridial neurotoxins, which include botulinum neurotoxins (BoNTs) and tetanus
neurotoxins, have evolved a remarkably sophisticated structure and molecular mechanism …

Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains

HP Hodgins, P Chen, B Lobb, X Wei… - Nature …, 2023 - nature.com
The analysis of microbial genomes from human archaeological samples offers a historic
snapshot of ancient pathogens and provides insights into the origins of modern infectious …

Multiobjective patient stratification using evolutionary multiobjective optimization

X Li, KC Wong - IEEE journal of biomedical and health …, 2017 - ieeexplore.ieee.org
One of the main challenges in modern medic-ine is to stratify patients for personalized care.
Many different clustering methods have been proposed to solve the problem in both …

Exploring the evolution of virulence factors through bioinformatic data mining

AC Doxey, MJ Mansfield, B Lobb - Msystems, 2019 - journals.asm.org
The molecular evolution of virulence factors is a central theme in our understanding of
bacterial pathogenesis and host-microbe interactions. Using bioinformatics and genome …

RAFTS3G: an efficient and versatile clustering software to analyses in large protein datasets

BT de Lima Nichio, AMR de Oliveira, CR de Pierri… - BMC …, 2019 - Springer
Background Clustering methods are essential to partitioning biological samples being useful
to minimize the information complexity in large datasets. Tools in this context usually …

Detecting signatures of positive selection against a backdrop of compensatory processes

PB Chi, WM Kosater, DA Liberles - Molecular Biology and …, 2020 - academic.oup.com
There are known limitations in methods of detecting positive selection. Common methods do
not enable differentiation between positive selection and compensatory covariation, a major …

Spacial models of malfunctioned protein complexes help to elucidate signal transduction critical for insulin release

K Walczewska-Szewc, W Nowak - Biosystems, 2019 - Elsevier
Mutations in gene KCNJ11 encoding the Kir6. 2 subunit of the ATP-sensitive potassium
channel (KATP), a representative of a quite complex biosystem, may affect insulin release …

[PDF][PDF] A genomic study of the invasive red alga Bangia atropurpurea (Mertens ex Roth) C. Agardh

V Poletto Borges - 2022 - uwspace.uwaterloo.ca
The phylum Rhodophyta comprises the red algae, which are morphologically diverse
organisms present in marine and freshwater environments. The red algae order, Bangiales …